[English] 日本語
Yorodumi
- PDB-2xu3: CATHEPSIN L WITH A NITRILE INHIBITOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xu3
TitleCATHEPSIN L WITH A NITRILE INHIBITOR
ComponentsCATHEPSIN L1
KeywordsHYDROLASE / DRUG DESIGN / THIOL PROTEASE
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / Collagen degradation / protein autoprocessing / fibronectin binding / collagen catabolic process / serpin family protein binding / collagen binding / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / Degradation of the extracellular matrix / multivesicular body / endocytic vesicle lumen / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / : / adaptive immune response / histone binding / Attachment and Entry / lysosome / apical plasma membrane / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-XU3 / Procathepsin L
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsBanner, D.W. / Benz, J.M. / Haap, W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Systematic Investigation of Halogen Bonding in Protein-Ligand Interactions.
Authors: Hardegger, L.A. / Kuhn, B. / Spinnler, B. / Anselm, L. / Ecabert, R. / Stihle, M. / Gsell, B. / Thoma, R. / Diez, J. / Benz, J. / Plancher, J.M. / Hartmann, G. / Banner, D.W. / Haap, W. / Diederich, F.
History
DepositionOct 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1865
Polymers24,1921
Non-polymers9944
Water6,720373
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.441, 49.394, 46.129
Angle α, β, γ (deg.)90.00, 105.13, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CATHEPSIN L1 / MAJOR EXCRETED PROTEIN / MEP


Mass: 24191.701 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 114-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07711, cathepsin L
#2: Chemical ChemComp-XU3 / (2S,4R)-4-(2-chlorophenyl)sulfonyl-1-[1-(5-chlorothiophen-2-yl)cyclopropyl]carbonyl-N-[1-(iminomethyl)cyclopropyl]pyrrolidine-2-carboxamide


Mass: 540.482 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23Cl2N3O4S2
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsORIGINAL COMPOUND (2S,4R)-4-(2-CHLORO-BENZENESULFONYL)-1-[1- (5-CHLORO-THIOPHEN-2-YL)- ...ORIGINAL COMPOUND (2S,4R)-4-(2-CHLORO-BENZENESULFONYL)-1-[1- (5-CHLORO-THIOPHEN-2-YL)-CYCLOPROPANECARBONYL-PYRROLIDINE-2- CARBOXYLIC ACID (1-CYANO-CYCLOPROPYL)-AMIDE REACTS WITH CYS TO BECOME XU3 VIA REDUCTION OF THE TRIPLE BOND

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.6 % / Description: NONE
Crystal growpH: 8.2 / Details: 0.1 M CITRIC ACID PH 3.5 25 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.9→50 Å / Num. obs: 139614 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.32 % / Biso Wilson estimate: 9.15 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.11
Reflection shellResolution: 0.9→1 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.25 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
REFMAC5.6.0077refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HWN

3hwn


Resolution: 0.9→44.53 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.593 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS GENERATED AT RIDING POSITIONS BY REFMAC. ZERO OCCUPANCY HYDROGENS REMOVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.15473 6706 5.1 %RANDOM
Rwork0.14183 ---
obs0.14248 125923 93.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.362 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.19 Å2
2--0.07 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 0.9→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 63 373 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212022
X-RAY DIFFRACTIONr_bond_other_d0.0010.021345
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9942776
X-RAY DIFFRACTIONr_angle_other_deg0.87833290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09725.41796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06715309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.323157
X-RAY DIFFRACTIONr_chiral_restr0.1010.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022370
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02414
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.62611440
X-RAY DIFFRACTIONr_sphericity_free7.9635374
X-RAY DIFFRACTIONr_sphericity_bonded2.93853295
LS refinement shellResolution: 0.9→0.923 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 408 -
Rwork0.367 8273 -
obs--82.62 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more